Folding@home GPU2 Client Examined

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There are quite a few distributed computing projects floating around the Web. These are very large-scale problems that require the processing power of large supercomputers, but can be broken up into small chunks that individual PCs can work on, and then send the data back to a central location for study. A good example is SETI@home.

SETI stands for Search for Extraterrestrial Intelligence and the projects take an enormous amount of radio telescope data, then processes and analyses the waveforms for strange anomalies. The right anomaly could be a signal from extraterrestrial intelligence, or so they hope. Each home PC running the SETI@home client processes a small chunk of data from a small piece of the sky, then sends the processed data back to a central server. Any interesting results are of course re-analyzed and studied by real people, and certainly no ETs have been found yet.

Perhaps the most popular of these distributed computing initiatives is Folding@home. It studies the process of protein self-assembly, or “folding,” a process which happens on an extremely short time scale. This sort of molecular simulation is computationally intensive, but it’s important to understanding the fundamentals of many diseases.

Protein mis-folding is thought to be responsible for Alzheimer’s, Mad Cow disease, ALS, and Parkinson’s disease. Understanding how proteins fold and mis-fold can go a long way toward helping us find a cure, and of course also helps us understand more about how biology works. You can read more about it at Stanford’s site.

A couple years ago, the FAH team started to beef up their computational power by developing new computing cores for streaming processors, including the PlayStation 3’s Cell processor and graphics processors. The original GPU core worked only with ATI’s Radeon X1900 class of GPUs, and interfaced with them through DirectX. This had limitations, but performance was still quite high.

Just last week, after a lot of waiting, Stanford finally released a beta of the “GPU2” client. This new client supports all Radeon HD 2400 and above cards, up to the Radeon HD 3870 X2. What’s more, DirectX is now bypassed, and the code interfaces to the card through ATI’s Compute Abstraction Layer (CAL). This should improve performance, compatibility, and enable FAH to support new cards more quickly.

Today we’ll examine this new client, and ask Dr. Vijay Pande, the Director of the Folding@home project, a few questions about it. Continued…

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